Related papers: Efficient Implementations of Molecular Dynamics Si…
This article introduces a highly parallel algorithm for molecular dynamics simulations with short-range forces on single node multi- and many-core systems. The algorithm is designed to achieve high parallel speedups for strongly…
We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up…
This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization…
Reactive molecular dynamics simulations are computationally demanding. Reaching spatial and temporal scales where interesting scientific phenomena can be observed requires efficient and scalable implementations on modern hardware. In this…
The performance of biomolecular molecular dynamics simulations has steadily increased on modern high performance computing resources but acceleration of the analysis of the output trajectories has lagged behind so that analyzing simulations…
Stochastic, spatial reaction-diffusion simulations have been widely used in systems biology and computational neuroscience. However, the increasing scale and complexity of simulated models and morphologies have exceeded the capacity of any…
Modern HPC systems are increasingly relying on greater core counts and wider vector registers. Thus, applications need to be adapted to fully utilize these hardware capabilities. One class of applications that can benefit from this increase…
Machine learning potentials have achieved great success in accelerating atomistic simulations. Many of them relying on atom-centered local descriptors are natural for parallelization. More recent message passing neural network (MPNN) models…
Parallelism of tight-binding molecular dynamics simulations is presented by means of the order-N electronic structure theory with the Wannier states, recently developed (J. Phys. Soc. Jpn. 69,3773 (2000)). An application is tested for…
The implicit 2D3V particle-in-cell (PIC) code developed to study the interaction of ultrashort pulse lasers with matter [G. M. Petrov and J. Davis, Computer Phys. Comm. 179, 868 (2008); Phys. Plasmas 18, 073102 (2011)] has been parallelized…
This report discusses the implementation of two parallel algorithms on a distributed memory system for studying vortex dynamics in type-II superconductors. These algorithms are the same as that implemented for classical molecular dynamics…
The integration of quantum chemical methods with high-performance computing is indispensable for handling large systems with modest accuracy or even small systems but with high accuracy. Continuing with the unified implementation of…
Molecular dynamics facilitates the simulation of a complex system to be analyzed at molecular and atomic levels. Simulations can last a long period of time, even months. Due to this cause the graphics processing units (GPUs) and multi-core…
For computational fluid dynamics (CFD) applications with a large number of grid points/cells, parallel computing is a common efficient strategy to reduce the computational time. How to achieve the best performance in the modern…
Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modelling of such systems.…
Comprehending the performance bottlenecks at the core of the intricate hardware-software interactions exhibited by highly parallel programs on HPC clusters is crucial. This paper sheds light on the issue of automatically asynchronous MPI…
Modern graphics processing units (GPUs) provide impressive computing resources, which can be accessed conveniently through the CUDA programming interface. We describe how GPUs can be used to considerably speed up molecular dynamics (MD)…
We present an efficient parallel algorithm for statistical Molecular Dynamics simulations of ion tracks in solids. The method is based on the Rare Event Enhanced Domain following Molecular Dynamics (REED-MD) algorithm, which has been…
We present an algorithm for cluster dynamics to efficiently simulate large systems on MIMD parallel computers with large numbers of processors. The method divides physical space into rectangular cells which are assigned to processors and…
The Simplex tableau has been broadly used and investigated in the industry and academia. With the advent of the big data era, ever larger problems are posed to be solved in ever larger machines whose architecture type did not exist in the…